The PDZ domain is a common structural domain of 80-90 amino-acids found in the signaling proteins of bacteria, yeast, plants, and animals. PDZ is an acronym combining the first letters of three proteins—post synaptic density protein (PSD95), Drosophila disc large tumor suppressor (DlgA), and zonula occludens-1 protein (zo-1)—which were first discovered to share the domain. PDZ domains are also referred to as DHR (Dlg homologous region) or GLGF (glycine-leucine-glycine-phenylalanine) (SEQ ID NO: 1) domains. These domains have been reported as helping to anchor transmembrane proteins to the cytoskeleton and hold together signaling complexes.
There are roughly 260 human PDZ domains, though since several PDZ domain containing proteins hold several domains, the actual number of PDZ proteins is closer to 180. Blazer et al., “Small Molecule Protein-Protein Interaction Inhibitors as CNS Theraputic Agents: Current Progress and Future Hurdles,” (Neuropsychopharmacology, 1-16, (2008)) (the teachings of which are incorporated herein by reference) states that “PDZ domains are important scaffolding components in many signaling systems, with an extensive role in the development and maintenance of both pre- and post-synaptic structures. Development of reversible small molecule inhibitors that target neuron-specific PDZ domains would provide useful tools to probe the many functions of these important scaffolds.” In a drug discovery program, stable, selective, high affinity chemical probes for PDZ domains will be useful in the identification and quantification of cellular protein therapeutic candidates having endogenous activity at the PDZ binding modules. Attention is drawn to Udugamasooriya et al., “Bridged Peptide Macrocycles as Ligands for PDZ Domain Proteins,” Organic Letters, 7(7):1203-1206 (2005), the teachings of which are incorporated herein by reference.
It has been reported that glutamate is the most prominent neurotransmitter in human physiology as present in over 50% of nervous tissue. Without being bound by any particular theory, it is believed that glutamate acts upon two classes of receptors, one containing a ligand-gated cation pore, called ionotropic glutamate receptors and the other class that responds to glutamate by mediating second-messenger proteins, called metabotropic glutamate receptors. The ionotropic receptors are further classified based upon preferential agonist binding/activation by N-methly-D-aspartate (NMDA-receptors), AMPA-receptors and kainate-receptors. All three glutamate receptors are permeable to sodium with the NMDA-R having a preference for calcium, and, when activated by glutamate, these ions enter the neuron through the central pore of the receptor, leading the neuron to depolarize.
Also noted are the following, the teachings of which are incorporated herein by reference (as are all references cited in this document):    1. Li et al., “Thermodynamic profiling of conformationally constrained cyclic ligands for the PDZ domain,”Bioorganic & Medicinal Chemistry Letters, 14, 1385-1388 (2004)    2. Guy et al. “Small molecule inhibition of PDZ-Domain interaction,” U.S. Pat. No. 7,141,600.    3. Chamila N. Rupasinghe and Mark R. Spaller, “The interplay between structure-based design and combinatorial chemistry,” Current Opinion in Chemical Biology, 10, 188-193 (2006).    4. Sharma et al., “Design, synthesis, and evaluation of linear and cyclic peptide ligands for PDZ10 of the multi-PDZ domain protein MUPP1,” Biochemistry, 46, 12709-12720 (2007).    5. Cui et al. “PDZ protein interactions underlying NMDA receptor mediated excitotoxicity and neuroprotection by PSD-95 inhibitors,” J. Neuroscience, 27, 9901-9915 (2007).    6. Klosi et al., “Bivalent peptides as PDZ domain ligands,” Bioorganic & Medicinal Chemistry Letters, 17, 6147-6150 (2007).    7. Saro et al. “A thermodynamic ligand binding study of the third PDZ domain (PDZ3) from the Mammalian Neuronal Protein PSD-95,” NIH, 46, 6340-6352. (2008).    8. Gomika et al. “A chemical library approach to organic-modified peptide ligands for PDZ domain proteins: A synthetic, thermodynamic and structural investigation,” Chem. Bio. Chem., 9, 1587-1589 (2008).    9. D. Gomika Udugamasooriya and Mark R. Spaller “Conformational constraint in protein ligand design and the inconsistency of binding entropy.” Biopolymers, 89, 653-667 (2008).    10. Tao Li, “Studies of ligand-protein interaction for the third PDZ domain (PDZ3) of mammalian post-synaptic density-95 (PSD-95)” (Jan. 1, 2005). ETD Collection for Wayne State University. Paper AAI3198697. http://digitalcommons.wayne.edu/dissertations/AAI3198697    11. Sutcliffe-Goulden et al., “Receptor-binding cyclic peptides and methods of use,” U.S. Ser. No. 11/198,884 (2005).
Further mention is made of Goun et al. “Molecular Transporters: Synthesis of Oligoguanidinium Transporters and Their Application to Drug Delivery and Real-Time Imaging,” ChemBioChem, 7:1479-1515 (2006) and Stewart et al., “Cell-penetrating peptides as deliver vehicles for biology and medicine,” Org. Biomol. Chem., 6:2242-2255 (2008), The Handbook of Cell-Penetrating Peptides, Second Edition, Ülo Langel, Ed, CRC (2006), and Cell-Penetrating Peptides: Processes and Applications, Ülo Langel, Ed, CRC (2002).
Various methods for producing cyclic peptides have been described. For example, chemical reaction protocols, such as those described in U.S. Pat. Nos. 4,033,940 and 4,102,877, have been devised to produce circularized peptides. In other techniques, biological and chemical methods are combined to produce cyclic peptides. Some methods involve first expressing linear precursors of cyclic peptides in cells (e.g., bacteria) to produce linear precursors of cyclic peptides and then adding of an exogenous agent such as a protease or a nucleophilic reagent to chemically convert these linear precursors into cyclic peptides. See, e.g., Camerero, J. A., and Muir, T. W., J. Am. Chem. Society. 121:5597 (1999); Wu, H. et al, Proc. Natl. Acad. Sci. USA, 95:9226 (1998).
Also noted are Martin Linhult et al., “Evaluation of different linker regions for multimerization and coupling chemistry for immobilization of a proteinaceous affinity ligand,” Protein Engineering, vol. 16 no. 12 pp. 1147-1152, Oxford University Press (2003).